celldetective 1.2.2__py3-none-any.whl → 1.2.2.post2__py3-none-any.whl

celldetective/__main__.py

@@ -1,405 +1,18 @@
 #!/usr/bin/env python3
 import sys
-from PyQt5.QtWidgets import QApplication, QSplashScreen, QMainWindow
+from PyQt5.QtWidgets import QApplication, QSplashScreen
 from PyQt5.QtGui import QPixmap
 from os import sep
 from celldetective.utils import get_software_location
-#from PyQt5.QtCore import QEventLoop
 from time import time, sleep
-import os
 #os.environ['QT_DEBUG_PLUGINS'] = '1'
 
-class AppInitWindow(QMainWindow):
-
-	"""
-	Initial window to set the experiment folder or create a new one.
-	"""
-
-	def __init__(self, parent_window=None):
-		super().__init__()
-
-		self.parent_window = parent_window
-		self.Styles = Styles()
-		self.init_styles()
-		self.setWindowTitle("celldetective")
-
-		self.n_threads = min([1,psutil.cpu_count()])
-
-		try:
-			subprocess.check_output('nvidia-smi')
-			print('NVIDIA GPU detected (activate or disable in Memory & Threads)...')
-			self.use_gpu = True
-		except Exception: # this command not being found can raise quite a few different errors depending on the configuration
-			print('No NVIDIA GPU detected...')
-			self.use_gpu = False
-			
-		self.soft_path = get_software_location()
-		self.onlyInt = QIntValidator()
-		self.setWindowIcon(QIcon(os.sep.join([self.soft_path,'celldetective','icons','logo.png'])))
-		center_window(self)
-		self._createActions()
-		self._createMenuBar()
-
-		app = QApplication.instance()
-		self.screen = app.primaryScreen()
-		self.geometry = self.screen.availableGeometry()
-		self.screen_width, self.screen_height = self.geometry.getRect()[-2:]
-
-		central_widget = QWidget()
-		self.vertical_layout = QVBoxLayout(central_widget)
-		self.vertical_layout.setContentsMargins(15,15,15,15)
-		self.vertical_layout.addWidget(QLabel("Experiment folder:"))
-		self.create_locate_exp_hbox()
-		self.create_buttons_hbox()
-		self.setCentralWidget(central_widget)
-		self.reload_previous_gpu_threads()
-		self.show()
-	
-	def closeEvent(self, event):
-		QApplication.closeAllWindows()
-		event.accept()
-		gc.collect()
-
-	def create_locate_exp_hbox(self):
-
-		self.locate_exp_layout = QHBoxLayout()
-		self.locate_exp_layout.setContentsMargins(0,5,0,0)
-		self.experiment_path_selection = QLineEdit()
-		self.experiment_path_selection.setAlignment(Qt.AlignLeft)	
-		self.experiment_path_selection.setEnabled(True)
-		self.experiment_path_selection.setDragEnabled(True)
-		self.experiment_path_selection.setFixedWidth(430)
-		self.experiment_path_selection.textChanged[str].connect(self.check_path_and_enable_opening)
-		self.foldername = os.getcwd()
-		self.experiment_path_selection.setPlaceholderText('/path/to/experiment/folder/')
-		self.locate_exp_layout.addWidget(self.experiment_path_selection, 90)
-
-		self.browse_button = QPushButton("Browse...")
-		self.browse_button.clicked.connect(self.browse_experiment_folder)
-		self.browse_button.setStyleSheet(self.button_style_sheet)
-		self.browse_button.setIcon(icon(MDI6.folder, color="white"))
-		self.locate_exp_layout.addWidget(self.browse_button, 10)
-		self.vertical_layout.addLayout(self.locate_exp_layout)
-
-
-	def _createMenuBar(self):
-
-		menuBar = self.menuBar()
-		menuBar.clear()
-		# Creating menus using a QMenu object
-
-		fileMenu = QMenu("File", self)
-		fileMenu.clear()
-		fileMenu.addAction(self.newExpAction)
-		fileMenu.addAction(self.openAction)
-
-		fileMenu.addMenu(self.OpenRecentAction)
-		self.OpenRecentAction.clear()
-		if len(self.recentFileActs)>0:
-			for i in range(len(self.recentFileActs)):
-				self.OpenRecentAction.addAction(self.recentFileActs[i])
-
-		fileMenu.addAction(self.openModels)
-		fileMenu.addSeparator()
-		fileMenu.addAction(self.exitAction)
-		menuBar.addMenu(fileMenu)
-
-		OptionsMenu = QMenu("Options", self)
-		OptionsMenu.addAction(self.MemoryAndThreadsAction)
-		menuBar.addMenu(OptionsMenu)
-
-		PluginsMenu = QMenu("Plugins", self)
-		PluginsMenu.addAction(self.CorrectAnnotationAction)
-		menuBar.addMenu(PluginsMenu)
-
-		helpMenu = QMenu("Help", self)
-		helpMenu.clear()
-		helpMenu.addAction(self.DocumentationAction)
-		helpMenu.addAction(self.SoftwareAction)
-		helpMenu.addSeparator()
-		helpMenu.addAction(self.AboutAction)
-		menuBar.addMenu(helpMenu)
-
-		#editMenu = menuBar.addMenu("&Edit")
-		#helpMenu = menuBar.addMenu("&Help")
-
-	def _createActions(self):
-		# Creating action using the first constructor
-		#self.newAction = QAction(self)
-		#self.newAction.setText("&New")
-		# Creating actions using the second constructor
-		self.openAction = QAction('Open...', self)
-		self.openAction.setShortcut("Ctrl+O")
-		self.openAction.setShortcutVisibleInContextMenu(True)
-
-		self.MemoryAndThreadsAction = QAction('Memory & Threads...')
-
-		self.CorrectAnnotationAction = QAction('Correct a segmentation annotation...')
-
-		self.newExpAction = QAction('New', self)
-		self.newExpAction.setShortcut("Ctrl+N")
-		self.newExpAction.setShortcutVisibleInContextMenu(True)
-		self.exitAction = QAction('Exit', self)
-
-		self.openModels = QAction('Open Models Location')
-		self.openModels.setShortcut("Ctrl+L")
-		self.openModels.setShortcutVisibleInContextMenu(True)
-
-		self.OpenRecentAction = QMenu('Open Recent')
-		self.reload_previous_experiments()
-
-		self.DocumentationAction = QAction("Documentation", self)
-		self.DocumentationAction.setShortcut("Ctrl+D")
-		self.DocumentationAction.setShortcutVisibleInContextMenu(True)
-
-		self.SoftwareAction = QAction("Software", self) #1st arg icon(MDI6.information)
-		self.AboutAction = QAction("About celldetective", self)
-
-		#self.DocumentationAction.triggered.connect(self.load_previous_config)
-		self.openAction.triggered.connect(self.open_experiment)
-		self.newExpAction.triggered.connect(self.create_new_experiment)
-		self.exitAction.triggered.connect(self.close)
-		self.openModels.triggered.connect(self.open_models_folder)
-		self.AboutAction.triggered.connect(self.open_about_window)
-		self.MemoryAndThreadsAction.triggered.connect(self.set_memory_and_threads)
-		self.CorrectAnnotationAction.triggered.connect(self.correct_seg_annotation)
-
-		self.DocumentationAction.triggered.connect(self.open_documentation)
-
-	def reload_previous_gpu_threads(self):
-
-		self.recentFileActs = []
-		self.threads_config_path = os.sep.join([self.soft_path,'celldetective','threads.json'])
-		print('Reading previous Memory & Threads settings...')
-		if os.path.exists(self.threads_config_path):
-			with open(self.threads_config_path, 'r') as f:
-				self.threads_config = json.load(f)
-			if 'use_gpu' in self.threads_config:
-				self.use_gpu = bool(self.threads_config['use_gpu'])
-				print(f'Use GPU: {self.use_gpu}...')
-			if 'n_threads' in self.threads_config:
-				self.n_threads = int(self.threads_config['n_threads'])
-				print(f'Number of threads: {self.n_threads}...')
-
-
-	def reload_previous_experiments(self):
-
-		recentExps = []
-		self.recentFileActs = []
-		if os.path.exists(os.sep.join([self.soft_path,'celldetective','recent.txt'])):
-			recentExps = open(os.sep.join([self.soft_path,'celldetective','recent.txt']), 'r')
-			recentExps = recentExps.readlines()
-			recentExps = [r.strip() for r in recentExps]
-			recentExps.reverse()
-			recentExps = list(dict.fromkeys(recentExps))
-			self.recentFileActs = [QAction(r,self) for r in recentExps]
-			for r in self.recentFileActs:
-				r.triggered.connect(lambda checked, item=r: self.load_recent_exp(item.text()))
-
-	def correct_seg_annotation(self):
-		
-		self.filename,_ = QFileDialog.getOpenFileName(self,"Open Image", "/home/", "TIF Files (*.tif)")
-		if self.filename!='':
-			print('Opening ',self.filename,' in napari...')
-			correct_annotation(self.filename)
-		else:
-			return None
-
-	def set_memory_and_threads(self):
-		
-		print('setting memory and threads')
-
-		self.ThreadsWidget = QWidget()
-		self.ThreadsWidget.setWindowTitle("Threads")
-		layout = QVBoxLayout()
-		self.ThreadsWidget.setLayout(layout)
-
-		self.threads_le = QLineEdit(str(self.n_threads))
-		self.threads_le.setValidator(self.onlyInt)
-
-		hbox = QHBoxLayout()
-		hbox.addWidget(QLabel('Parallel threads: '), 33)
-		hbox.addWidget(self.threads_le, 66)
-		layout.addLayout(hbox)
-
-		self.use_gpu_checkbox = QCheckBox()
-		hbox2 = QHBoxLayout()
-		hbox2.addWidget(QLabel('Use GPU: '), 33)
-		hbox2.addWidget(self.use_gpu_checkbox, 66)
-		layout.addLayout(hbox2)
-		if self.use_gpu:
-			self.use_gpu_checkbox.setChecked(True)
-
-		self.validateThreadBtn = QPushButton('Submit')
-		self.validateThreadBtn.setStyleSheet(self.button_style_sheet)
-		self.validateThreadBtn.clicked.connect(self.set_threads)
-		layout.addWidget(self.validateThreadBtn)
-		center_window(self.ThreadsWidget)
-		self.ThreadsWidget.show()
-
-	def set_threads(self):
-		self.n_threads = int(self.threads_le.text())
-		self.use_gpu = bool(self.use_gpu_checkbox.isChecked())
-		dico = {"use_gpu": self.use_gpu, "n_threads": self.n_threads}
-		with open(self.threads_config_path, 'w') as f:
-			json.dump(dico, f, indent=4)
-		self.ThreadsWidget.close()
-
-
-	def open_experiment(self):
-		print('ok')
-		self.browse_experiment_folder()
-		if self.experiment_path_selection.text()!='':
-			self.open_directory()
-
-	def load_recent_exp(self, path):
-		
-		self.experiment_path_selection.setText(path)
-		print(f'Attempt to load experiment folder: {path}...')
-		self.open_directory()
-
-	def open_about_window(self):
-		self.about_wdw = AboutWidget()
-		self.about_wdw.show()
-
-	def open_documentation(self):
-		doc_url = QUrl('https://celldetective.readthedocs.io/')
-		QDesktopServices.openUrl(doc_url)
-
-	def open_models_folder(self):
-		path = os.sep.join([self.soft_path,'celldetective','models',os.sep])
-		try:
-			subprocess.Popen(f'explorer {os.path.realpath(path)}')
-		except:
-
-			try:
-				os.system('xdg-open "%s"' % path)
-			except:
-				return None
-
-
-		#os.system(f'start {os.path.realpath(path)}')
-
-	def create_buttons_hbox(self):
-
-		self.buttons_layout = QHBoxLayout()
-		self.buttons_layout.setContentsMargins(30,15,30,5)
-		self.new_exp_button = QPushButton("New")
-		self.new_exp_button.clicked.connect(self.create_new_experiment)
-		self.new_exp_button.setStyleSheet(self.button_style_sheet_2)
-		self.buttons_layout.addWidget(self.new_exp_button, 50)
-
-		self.validate_button = QPushButton("Open")
-		self.validate_button.clicked.connect(self.open_directory)
-		self.validate_button.setStyleSheet(self.button_style_sheet)
-		self.validate_button.setEnabled(False)
-		self.validate_button.setShortcut("Return")
-		self.buttons_layout.addWidget(self.validate_button, 50)
-		self.vertical_layout.addLayout(self.buttons_layout)
-
-	def check_path_and_enable_opening(self):
-		
-		"""
-		Enable 'Open' button if the text is a valid path.
-		"""
-
-		text = self.experiment_path_selection.text()
-		if (os.path.exists(text)) and os.path.exists(os.sep.join([text,"config.ini"])):
-			self.validate_button.setEnabled(True)
-		else:
-			self.validate_button.setEnabled(False)
-
-	def init_styles(self):
-
-		"""
-		Initialize styles.
-		"""
-		
-		self.qtab_style = self.Styles.qtab_style
-		self.button_style_sheet = self.Styles.button_style_sheet
-		self.button_style_sheet_2 = self.Styles.button_style_sheet_2
-		self.button_style_sheet_2_not_done = self.Styles.button_style_sheet_2_not_done
-		self.button_style_sheet_3 = self.Styles.button_style_sheet_3
-		self.button_select_all = self.Styles.button_select_all
-
-	def set_experiment_path(self, path):
-		self.experiment_path_selection.setText(path)
-
-	def create_new_experiment(self):
-
-		print("Configuring new experiment...")
-		self.new_exp_window = ConfigNewExperiment(self)
-		self.new_exp_window.show()
-
-	def open_directory(self):
-
-		self.exp_dir = self.experiment_path_selection.text().replace('/', os.sep)
-		print(f"Setting current directory to {self.exp_dir}...")
-
-		wells = glob(os.sep.join([self.exp_dir,"W*"]))
-		self.number_of_wells = len(wells)
-		if self.number_of_wells==0:
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Critical)
-			msgBox.setText("No well was found in the experiment folder.\nPlease respect the W*/ nomenclature...")
-			msgBox.setWindowTitle("Error")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				return None
-		else:
-			if self.number_of_wells==1:
-				print(f"Found {self.number_of_wells} well...")
-			elif self.number_of_wells>1:
-				print(f"Found {self.number_of_wells} wells...")
-			number_pos = []
-			for w in wells:
-				position_folders = glob(os.sep.join([w,f"{w.split(os.sep)[-1][1]}*", os.sep]))
-				number_pos.append(len(position_folders))
-			print(f"Number of positions per well: {number_pos}")
-			
-			with open(os.sep.join([self.soft_path,'celldetective','recent.txt']), 'a+') as f:
-				f.write(self.exp_dir+'\n')
-
-			self.control_panel = ControlPanel(self, self.exp_dir)
-			self.control_panel.show()
-
-			self.reload_previous_experiments()
-			self._createMenuBar()
-
-
-	def browse_experiment_folder(self):
-
-		"""
-		Locate an experiment folder. If no configuration file is in the experiment, display a warning.
-		"""
-
-		self.foldername = str(QFileDialog.getExistingDirectory(self, 'Select directory'))
-		if self.foldername!='':
-			self.experiment_path_selection.setText(self.foldername)
-		else:
-			return None
-		if not os.path.exists(self.foldername+"/config.ini"):
-			msgBox = QMessageBox()
-			msgBox.setIcon(QMessageBox.Warning)
-			msgBox.setText("No configuration can be found in the selected folder...")
-			msgBox.setWindowTitle("Warning")
-			msgBox.setStandardButtons(QMessageBox.Ok)
-			returnValue = msgBox.exec()
-			if returnValue == QMessageBox.Ok:
-				self.experiment_path_selection.setText('')
-				return None
-
 if __name__ == "__main__":
 
-	# import ctypes
-	# myappid = 'mycompany.myproduct.subproduct.version' # arbitrary string
-	# ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 	splash=True
 	print('Loading the libraries...')
 
 	App = QApplication(sys.argv)
-	#App.setWindowIcon(QIcon(os.sep.join([get_software_location(),'celldetective','icons','mexican-hat.png'])))
 	App.setStyle("Fusion")
 
 	if splash:
@@ -414,23 +27,8 @@ if __name__ == "__main__":
 			App.processEvents()
 
 	from PyQt5.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QCheckBox, QHBoxLayout, QLabel, QLineEdit, QPushButton, QMessageBox, QMenu, QAction
-	from PyQt5.QtCore import Qt, QUrl
 	from PyQt5.QtGui import QIcon, QDesktopServices, QIntValidator
-	from glob import glob
-	from superqt.fonticon import icon
-	from fonticon_mdi6 import MDI6
-	import gc
-	from celldetective.gui import Styles, ControlPanel, ConfigNewExperiment
-	from celldetective.gui.gui_utils import center_window
-	import subprocess
-	import os
-	from celldetective.gui.about import AboutWidget
-	from celldetective.io import correct_annotation
-	import psutil
-	import subprocess
-	import json
-	# import matplotlib
-	# matplotlib.rcParams.update({'font.size': 8})
+	from celldetective.gui.InitWindow import AppInitWindow
 
 	print('Libraries successfully loaded...')